Comparing On-site to off-site biomass collection for dehalococcoides biomarker gene quantification to predict in situ chlorinated ethene detoxification potential

Environmental Science and Technology

Volumn 44, Issue 13, 2010, Pages 5127-5133

  Ritalahti, Kirsti M ^a   Hatt, Janet K ^c   Lugmayr, Veronica ^a   Henn, Keith ^d   Petrovskis, Erik A ^e   Ogles, Dora M ^f   Davis, Greg A ^f   Yeager, Chris M ^g   Lebrón, Carmen A ^h   Löffler, Frank E ^a,b,i  

^a UNIVERSITY OF TENNESSEE   (United States)

^b University of Tennessee   (United States)

^c Georgia Institute of Technology   (United States)

^d TETRA TECH INC   (United States)

^e GEOSYNTEC CONSULTANTS   (United States)

^f Microbial Insights   (United States)

^g SAVANNAH RIVER NATIONAL LABORATORY   (United States)

^h NAVFAC Engineering Service Center   (United States)

ⁱ OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL LABORATORIES; AQUEOUS SAMPLES; BIO-AUGMENTATION; BIOSTIMULATION; CHLORINATED ETHENES; CONTAMINATED AQUIFER; DEHALOCOCCOIDES; DNA EXTRACTION; DNA YIELDS; ETHENE FORMATION; IN-SITU; LABORATORY STUDIES; MEMBRANE FILTERS; QUANTITATIVE REAL TIME PCR; REDUCTIVE DEHALOGENASES; TARGET CELLS; TARGET GENES; VACUUM FILTRATION; VINYL CHLORIDES;

AQUIFERS; BIOMASS; CHLORINE COMPOUNDS; DETOXIFICATION; DNA; ETHYLENE; GROUNDWATER POLLUTION; GROUNDWATER RESOURCES; HYDROGEOLOGY; LABORATORIES; MICROFILTRATION; PROJECTILES; VACUUM;

GENES;

BIOLOGICAL MARKER; DNA; ETHYLENE; GROUND WATER; VINYL CHLORIDE;

AQUIFER; BACTERIUM; BIOMARKER; BIOMASS; BIOMONITORING; COMPARATIVE STUDY; DETOXIFICATION; ETHYLENE; GROUNDWATER POLLUTION; POLYMERASE CHAIN REACTION; REAL TIME; VOLUME;

ARTICLE; BACTERIUM; BIOMASS; CONTROLLED STUDY; DEHALOCOCCOIDES; DETOXIFICATION; DNA EXTRACTION; FILTRATION; MARKER GENE; MEMBRANE FILTER; MONITORING; NONHUMAN; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; VACUUM;

BIOLOGICAL MARKERS; BIOMASS; CHLORINE; CHLOROFLEXI; DNA; DNA, BACTERIAL; ETHYLENES; FILTRATION; MODELS, STATISTICAL; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; WATER MICROBIOLOGY; WATER POLLUTANTS; WATER PURIFICATION;

DEHALOCOCCOIDES;

EID: 77954253938     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/es100408r     Document Type: Article

References (32)

1. Amos, B. K.; Suchomel, E. J.; Pennell, K. D.; Löffler, F. E. Correlating microbial activity and distribution with enhanced contaminant dissolution from a NAPL source zone Water Res. 2008, 42, 2963-2974
2. Freedman, D. L.; Gossett, J. M. Biological reductive dechlorination of tetrachloroethylene and trichloroethylene to ethylene under methanogenic conditions Appl. Environ. Microbiol. 1989, 55, 2144-2151
3. Maymó-Gatell, X.; Chien, Y.-T.; Gossett, J. M.; Zinder, S. H. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene Science 1997, 276, 1568-1571
4. He, J.; Ritalahti, K. M.; Yang, K.-L.; Koenigsberg, S. S.; Löffler, F. E. Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium Nature 2003, 424, 62-65
5. Müller, J. A.; Rosner, B. M.; Von Abendroth, G.; Meshulam-Simon, G.; McCarty, P. L.; Spormann, A. M. Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain VS and its environmental distribution Appl. Environ. Microbiol. 2004, 70, 4880-4888
6. Sung, Y.; Ritalahti, K. M.; Apkarian, R. P.; Löffler, F. E. Quantitative PCR confirms purity of strain GT, a novel trichloroethene (TCE)-to-ethene respiring Dehalococcoides isolate Appl. Environ. Microbiol. 2006, 72, 1980-1987
7. Ritalahti, K. M.; Amos, B. K.; Sung, Y.; Wu, Q.; Koenigsberg, S. S.; Löffler, F. E. Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains Appl. Environ. Microbiol. 2006, 72, 2765-2774
8. Holmes, V. F.; He, J.; Lee, P. K. H.; Alvarez-Cohen, L. Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes Appl. Environ. Microbiol. 2006, 72, 5877-5883
9. Puls, R. W.; Barcelona, M. J. Low-Flow (minimal drawdown) ground water sampling procedures U.S. EPA, Ground Water Issue, Publication Number EPA/540/S-95/504 1996, 1-12
10. Yeskis, D.; Zavala, B. Ground-water sampling guidelines for superfund and RCRA project managers Ground Water Forum Issue Paper EPA 542-S-02-001 2002, 1-53
11. Cupples, A. M. Real-time PCR quantification of Dehalococcoides populations: methods and applications J. Microbiol. Methods 2008, 72, 1-11
12. Herzog, B.; Pennino, J.;; Nielsen, G. Chapter 11: Ground-water sampling. In Practical handbook of ground water monitoring; Nielsen, D. M., Ed.; CRC Press: Boca Raton, FL, 1991; pp 449 - 500.
13. Yeates, C.; Gillings, M. R.; Davison, A. D.; Altavilla, N.; Veal, D. A. Methods for microbial DNA extraction from soil for PCR amplification Biol. Procedures Online 1998, 1, 40-47
14. Levine, U. Y.; Crump, B. C. Bacterioplankton community composition in flowing waters of the Ipswich River watershed Biol. Bull. 2002, 203, 251-2
15. Short, S. M.; Jenkins, B. D.; Zehr, J. P. Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake Bay Appl. Environ. Microbiol. 2004, 70, 2186-2192
16. Somerville, C. C.; Knight, I. T.; Straube, W. L.; Colwell, R. R. Simple, rapid method for direct isolation of nucleic acids from aquatic environments Appl. Environ. Microbiol. 1989, 55, 548-554
17. Ritalahti, K. M.; Löffler, F. E.; Rasch, E. E.; Koenigsberg, S. S. Bioaugmentation for chlorinated ethene detoxification: Bioaugmentation and molecular diagnostics in the bioremediation of chlorinated ethene-contaminated sites Ind. Biotechnol. 2005, 1, 114-118
18. Löffler, F. E.; Edwards, E. A. Harnessing microbial activities for environmental cleanup Curr. Opin. Biotechnol. 2006, 17, 274-284
19. Duhamel, M.; Edwards, E. A. Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides FEMS Microbiol. Ecol. 2006, 58, 538-549
20. Sambrook, J.; Russell, D. W. Molecular cloning: A laboratory manual, 3rd ed.; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 2001.
21. Ritalahti, K. M.; Hatt, J. K.; Petrovskis, E.; Löffler, F. E. Groundwater sampling for nucleic acid biomarker analysis. In Handbook of Hydrocarbon and Lipid Microbiology; Timmis, K. N., Ed.; Springer: Berlin, 2009; pp 3407 - 3418.
22. Ausubel, F.; Brent, R.; Kingston, R. E.; Moore, D. D.; Seidman, J. G.; Smith, J. A.; Struhl, K. Short Protocols in Molecular Biology, 3rd ed.; John Wiley & Sons, Inc.: New York, NY, 1997.
23. Nolan, T.; Hands, R. E.; Bustin, S. A. Quantification of mRNA using real-time RT-PCR Nat. Protoc. 2006, 1, 1559-1582
24. Bustin, S. A.; Nolan, T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction J. Biomol. Technol. 2004, 15, 155-166
25. Bustin, S. A.; Benes, V.; Nolan, T.; Pfaffl, M. W. Quantitative real-time RT-PCR- a perspective J. Mol. Endocrinol. 2005, 34, 597-601
26. Bradley, P. M.; Chapelle, F. H. Acetogenic microbial degradation of vinyl chloride Environ. Sci. Technol. 2000, 34, 2761-2763
27. Bradley, P. M. History and ecology of chlororethene biodegradation: a review Biorem. J. 2003, 7, 81-109
28. Wiedemeier, T. H.; Swanson, M. A.; Moutoux, D. E.; Gordon, E. K.; Wilson, J. T.; Wilson, B. H.; Kampbell, D. H.; Haas, P. E.; Miller, R. N.; Hansen, J. E.; Chapelle, F. H. Technical Protocol for Evaluating Natural Attenuation of Chlorinated Solvents in Ground Water; EPA/600/R-98/128; 1998. http://www.epa.gov/superfund/health/conmedia/gwdocs/protocol.htm.
29. Hendrickson, E. R.; Payne, J. A.; Young, R. M.; Starr, M. G.; Perry, M. P.; Fahnestock, S.; Ellis, D. E.; Ebersole, R. C. Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe Appl. Environ. Microbiol. 2002, 68, 485-495
30. van der Zaan, B.; Hannes, F.; Hoekstra, N.; Rijnaarts, H.; de Vos, W. M.; Smidt, H.; Gerritse, J. Correlation of Dehalococcoides 16S rRNA and chloroethene-reductive dehalogenase genes with geochemical conditions in chloroethene-contaminated groundwater. Appl. Environ. Microbiol. 2010, 76, 843-850
31. Lu, X.; Wilson, J. T.; Kampbell, D. H. Relationship between Dehalococcoides DNA in ground water and rates of reductive dechlorination at field scale Water Res. 2006, 40, 3131-3140
32. Gossett, J. M. Sustained aerobic oxidation of vinyl chloride at low oxygen concentrations. Environ. Sci. Technol. 2010, 44, 1405-1411